I have my empire policy set to never use super lasers to destroy enemy colonies. I then equipped my capital ships with super lasers with the intent of using them to take out tough bases and capital ships.
My first opportunity to test, however, resulted in a blown up planet that I think had a mining base on it, though it might have been a colony moon. My fleet was set to automated attack orders against an enemy empire. The last order given was to attack a mining base in the same system, but this was less than a minute before I flipped over to check on them to see an exploding planet.
Unfortunately, my game barfed from a memory leak shortly thereafter, so I don't have a recent save. That said, I imagine it could have been one of the following scenarios:
1. The empire policy only applies to the actual Planet Destroyer ships, not just the super laser.
2. The empire policy only applies to actual colonies, not planets/moons with bases on them.
3. The empire policy works, but in the process of blowing up a mining base with a super laser the planet it's on is also destroyed simply as collateral damage.
Needless to say, my empire took a reputation hit from admired to dubious. I was actually somewhat amused and inclined to keep the game going, dismissing the admiral for criminal negligence, suing for peace with the empire I had just wronged, and immediately redesigning my capital ships. Alas, I can't justify intentionally wasting a planet when I pick it back of from an earlier auto-save just to replicate the scenario.